The shadows didn't put bombs all over a planet with no one knowing or put space bugs on planetary leaders. From a outright War perspective the Shadows were more powerful than their allies obviously, but the allies are capable of stuff the shadows weren't, and I'd say the ability to control/threaten a whole planet like that makes them more powerful at what they do (behind the scenes evil and manipulation as opposed to outright conflict) than their masters, even though the Shadows were supposed to be good at stuff like that. The allies just seem to have been written as almost all powerful, atleast in their manipulations of the centauri, and not even the Shadows were able to do that.